Setup

FastQC Summary

Summary statistics for all libraries
Filename Total Flagged As Poor Quality Sequence Length %GC
1_non_mutant_Q96_K97del_6mth_10_03_2016_S1_fem_R1.fastq.gz 45,249,907 0 150-150 46
1-MORGAN-6P-PN1_S2_R1_001.fastq.gz 26,302,897 0 76-76 44
11__-_5_R1.fq.gz 21,273,771 0 35-76 45
12__-_4_R1.fq.gz 22,071,800 0 35-76 45
13__-_3_R1.fq.gz 1.7e+07 0 35-76 45
14__-_2_R1.fq.gz 24,270,286 0 35-76 45
15__-_1_R1.fq.gz 25,647,352 0 35-76 45
2_non_mutant_Q96_K97del_6mth_10_03_2016_S2_fem_R1.fastq.gz 39,114,762 0 150-150 45
2-MORGAN-6P-PN2_S5_R1_001.fastq.gz 45,259,313 0 76-76 44
3_non_mutant_Q96_K97del_6mth_10_03_2016_S3_fem_R1.fastq.gz 42,797,663 0 150-150 45
3-MORGAN-6P-PN3_S10_R1_001.fastq.gz 29,287,775 0 76-76 44
4_non_mutant_K97Gfs_6mth_10_03_2016_S1_fem_R1.fastq.gz 46,369,672 0 150-150 44
4-MORGAN-6P-PN4_S8_R1_001.fastq.gz 32,052,087 0 76-76 43
5_non_mutant_K97Gfs_6mth_10_03_2016_S2_fem_R1.fastq.gz 39,006,553 0 101-101 43
6_non_mutant_K97Gfs_6mth_10_03_2016_S3_fem_R1.fastq.gz 83,077,374 0 150-150 44
Ps2Ex3M1_WT_6month_07_07_2016_F3_79_Fem_R1.fastq.gz 27,979,654 0 150-150 47
Ps2Ex3M1_WT_6month_07_07_2016_F3_86_Fem_R1.fastq.gz 32,642,121 0 150-150 47
Ps2Ex3M1_WT_6month_07_07_2016_F3_88_Fem_R1.fastq.gz 34,587,957 0 150-150 48
Ps2Ex3M1_WT_6month_07_07_2016_F3_95_Fem_R1.fastq.gz 32,013,598 0 150-150 46
W1_1.fq.gz 46,329,465 0 150-150 43
W1_2.fq.gz 46,329,465 0 150-150 44
W2_1.fq.gz 44,097,195 0 150-150 44
W2_2.fq.gz 44,097,195 0 150-150 44
W3_1.fq.gz 45,464,120 0 150-150 43
W3_2.fq.gz 45,464,120 0 150-150 44
W4_1.fq.gz 53,931,526 0 150-150 43
W4_2.fq.gz 53,931,526 0 150-150 44
W5_1.fq.gz 41,480,106 0 150-150 43
W5_2.fq.gz 41,480,106 0 150-150 43

Read Totals

Library Sizes ranged between 17,004,294 and 83,077,374 reads.

Read totals for each library. Duplicated reads are conventionally an high overestimate at this point.

FastQC Summary

Summary of FastQC flags for each parameter

Per Base Sequence Quality

Heatmap showing mean base qualities for each library

Per Sequence Quality Scores

Heatmap showing mean sequence qualities for each library

Per Base Sequence Content

Heatmap of summed base distributions along each read

Per Sequence GC Content

GC Content Heatmap normalised to theoretical GC content in the Hsapiens Genome

GC Content Distributions for all reads showing theoretical GC content from the Hsapiens Genome

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented Summary

Total overrepresented sequences for each library

Overrepresented Sequences

## Overrepresented_sequences missing from 1-MORGAN-6P-PN1_S2_R1_001.fastq.gz
## Overrepresented_sequences missing from 11__-_5_R1.fq.gz
## Overrepresented_sequences missing from 12__-_4_R1.fq.gz
## Overrepresented_sequences missing from 13__-_3_R1.fq.gz
## Overrepresented_sequences missing from 14__-_2_R1.fq.gz
## Overrepresented_sequences missing from 15__-_1_R1.fq.gz
## Overrepresented_sequences missing from 2-MORGAN-6P-PN2_S5_R1_001.fastq.gz
## Overrepresented_sequences missing from 3-MORGAN-6P-PN3_S10_R1_001.fastq.gz
## Overrepresented_sequences missing from 4-MORGAN-6P-PN4_S8_R1_001.fastq.gz
## Overrepresented_sequences missing from W1_1.fq.gz
## Overrepresented_sequences missing from W1_2.fq.gz
## Overrepresented_sequences missing from W2_1.fq.gz
## Overrepresented_sequences missing from W2_2.fq.gz
## Overrepresented_sequences missing from W3_1.fq.gz
## Overrepresented_sequences missing from W3_2.fq.gz
## Overrepresented_sequences missing from W4_1.fq.gz
## Overrepresented_sequences missing from W4_2.fq.gz
## Overrepresented_sequences missing from W5_1.fq.gz
## Overrepresented_sequences missing from W5_2.fq.gz
Summary of Overrepresented Sequences in all files. A maximum of 30 seqences are shown.
Sequence Total Present In Overall Percentage Max_Percentage Possible_Source
CCGCTGTATTACTCAGGCTGCACTGCAGTGTCTATTCACAGGCGCGATCC 1,981,001 10 0.176% 0.68% No Hit
CGCTGTATTACTCAGGCTGCACTGCAGTGTCTATTCACAGGCGCGATCCC 1,705,784 6 0.151% 0.67% No Hit
GTGGGTTCAGGTAATTAATTTAAAGCTACTTTCGTGTTTGGGCCTCTAGC 1,478,805 4 0.131% 1.72% No Hit
GGTTCAGGTAATTAATTTAAAGCTACTTTCGTGTTTGGGCCTCTAGCATC 1,213,039 4 0.107% 1.09% No Hit
CTGAAGTCTTGGAGCTCGACTTCCCTACGTTTCGCCTACAAATGTTGCCT 900,121 6 0.080% 0.36% No Hit
GGGGTGTACGAAGCTGAACTTTTATTCATCTCCCAGACAACCAGCTATTG 751,501 4 0.067% 1.07% No Hit
GGGTTCAGGTAATTAATTTAAAGCTACTTTCGTGTTTGGGCCTCTAGCAT 662,397 4 0.059% 0.78% No Hit
GTTCAGGTAATTAATTTAAAGCTACTTTCGTGTTTGGGCCTCTAGCATCT 646,200 4 0.057% 0.56% No Hit
CTTAGACGACCTGGTAGTCCAAGGCTCCCCCAGGAGCACCATATCGATAC 516,132 7 0.046% 0.27% No Hit
CCTCCTTCAAGTATTGTTTCATGTTACATTTTCGTATATTCTGGGGTAGA 465,262 4 0.041% 0.58% No Hit
CTCCTGAAAAGGTTGTATCCTTTGTTAAAGGGGCTGTACCCTCTTTAACT 439,796 3 0.039% 0.69% No Hit
GGGCCTCTAGCATCTAAAAGCGTATAACAGTTAAAGGGCCGTTTGGCTTT 421,995 3 0.037% 0.62% No Hit
CGGGTCGGGTGGGTGGCCGGCATCACCGCGGACCTCGGGCGCCCTTTTGG 417,361 4 0.037% 0.73% No Hit
GCTGTATTACTCAGGCTGCACTGCAGTGTCTATTCACAGGCGCGATCCCA 392,887 6 0.035% 0.15% No Hit
GTATTACTCAGGCTGCACTGCAGTGTCTATTCACAGGCGCGATCCCACTA 379,000 6 0.034% 0.15% No Hit
GGGTGTACGAAGCTGAACTTTTATTCATCTCCCAGACAACCAGCTATTGC 351,669 4 0.031% 0.43% No Hit
CGGGTCGGGTGGGTAGCCGGCATCACCGCGGACCTCGGGCGCCCTTTTGG 346,616 4 0.031% 0.57% No Hit
CCCGCTGTATTACTCAGGCTGCACTGCAGTGTCTATTCACAGGCGCGATC 317,427 4 0.028% 0.39% No Hit
CTCCGACCTGGGCCGGTTCACCCCTCCTTAGACGACCTGGTAGTCCAAGG 244,650 4 0.022% 0.12% No Hit
ATTACTCAGGCTGCACTGCAGTGTCTATTCACAGGCGCGATCCCACTACT 202,097 3 0.018% 0.13% No Hit
GGCCTCTAGCATCTAAAAGCGTATAACAGTTAAAGGGCCGTTTGGCTTTA 189,815 2 0.017% 0.37% No Hit
AGCTGGGGAGATCCGCGAGAAGGGCCCGGCGCACGTCCAGAGTCGCCGCC 177,147 3 0.016% 0.23% No Hit
GGTCGGGTGGGTGGCCGGCATCACCGCGGACCTCGGGCGCCCTTTTGGAC 172,979 3 0.015% 0.25% No Hit
GGTGTACGAAGCTGAACTTTTATTCATCTCCCAGACAACCAGCTATTGCC 172,617 4 0.015% 0.20% No Hit
GTCCCCCACTACCAGAAATTATGCAGTCGAGATTCCCACATTTGGGGAAT 165,358 3 0.015% 0.19% No Hit
GTCTGAAGTCTTGGAGCTCGACTTCCCTACGTTTCGCCTACAAATGTTGC 161,482 3 0.014% 0.24% No Hit
GGCCCGGCGCACGTCCAGAGTCGCCGCCGCGCACCGCAGCGCATCCCCCC 159,243 2 0.014% 0.36% No Hit
GCCCACTACGACAACGTGTTTTGTAAATTATGATCTTTATTCTCCTGAAA 154,577 2 0.014% 0.24% No Hit
GCTCGGGTGTCTACATCCATTCCTACAGTGAATATGTGATGGGCTCATAC 146,042 3 0.013% 0.20% No Hit
GGCCCACTACGACAACGTGTTTTGTAAATTATGATCTTTATTCTCCTGAA 133,144 2 0.012% 0.22% No Hit

Adapter Content

Universal Adapter Content

Kmer Content

## Kmer_Content missing from 11__-_5_R1.fq.gz
## Kmer_Content missing from 12__-_4_R1.fq.gz
## Kmer_Content missing from 13__-_3_R1.fq.gz
## Kmer_Content missing from 14__-_2_R1.fq.gz
## Kmer_Content missing from 15__-_1_R1.fq.gz
## Kmer_Content missing from W1_1.fq.gz
## Kmer_Content missing from W1_2.fq.gz
## Kmer_Content missing from W2_1.fq.gz
## Kmer_Content missing from W2_2.fq.gz
## Kmer_Content missing from W3_1.fq.gz
## Kmer_Content missing from W3_2.fq.gz
## Kmer_Content missing from W4_1.fq.gz
## Kmer_Content missing from W4_2.fq.gz
## Kmer_Content missing from W5_1.fq.gz
## Kmer_Content missing from W5_2.fq.gz
Summary of Overrepresented Kmers in all files. A maximum of 30 Kmers are shown.
Sequence Max_Obs/Exp_Position Total Abundance Present In
TACTCAG 9 711,780 6
TCTTGGA 7 438,295 6
AGTCTTG 5 431,595 6
TTGGAGC 9 427,330 6
GAAGTCT 3 418,095 6
CCGCTGT 1 396,830 6
GTCTTGG 6 395,470 6
CTGAAGT 1 443,565 5
GGGTTCA 3 389,235 4
TGAAGTC 2 361,460 4
CTTGGAG 8 353,990 4
GTGGGTT 1 317,480 4
TGGGTTC 2 280,610 4
GTCGGGT 4 205,980 4
GGGTCGG 2 184,535 4
CGGGTCG 1 139,940 4
CGCGGGT 68 33,745 4
AACGCCG 55 31,180 4
TAACGCC 54 30,900 4
CGCCGGA 60 30,835 4
GGATCGC 64 30,815 4
CGGATCG 63 29,330 4
CCGGAAC 1 29,035 4
TCGCGGG 67 28,615 4
CGGAACC 2 27,460 4
GATCGCG 65 27,035 4
ATCGCGG 66 26,935 4
TTACTCA 9 491,075 3
CTGTATT 4 480,420 3
TATTACT 7 454,685 3